Preprocessing QC statistics ¶

Sagy, July 2024 - Opera 18 days REIMAGED¶

In [6]:
%load_ext autoreload
%autoreload 2

The autoreload extension is already loaded. To reload it, use:
  %reload_ext autoreload
In [7]:
import os
MOMAPS_HOME = '/home/labs/hornsteinlab/Collaboration/MOmaps'
MOMAPS_DATA_HOME = '/home/labs/hornsteinlab/Collaboration/MOmaps'
LOGS_PATH = os.path.join(MOMAPS_DATA_HOME, "outputs/preprocessing/Opera18Days_Reimaged/logs/")
PLOT_PATH = os.path.join(MOMAPS_DATA_HOME, "outputs/preprocessing/Opera18Days_Reimaged/logs/plots")
os.chdir(MOMAPS_HOME)
import numpy as np
import pandas as pd
import seaborn as sns
import matplotlib.pyplot as plt
plt.rcParams["image.cmap"] = "Set1"
from src.common.lib.preprocessing_utils import rescale_intensity
from src.common.lib.images_qc import *
import contextlib
import io
import matplotlib
import warnings
warnings.filterwarnings('ignore', category=pd.core.common.SettingWithCopyWarning)
from src.common.lib.qc_config_tmp import *
from src.common.lib.image_sampling_utils import *
from matplotlib.colors import LinearSegmentedColormap
In [8]:
pd.__version__
Out[8]:
'1.3.5'
In [9]:
df = log_files_qc(LOGS_PATH,only_wt_cond=False, filename_split='-',site_location=0)
df_dapi = df[df.marker=='DAPI']
df_target = df[df.marker!='DAPI']

reading logs of batch2
reading logs of batch1

Total of 2 files were read.
Before dup handeling  (120169, 22)
After duplication removal #1: (120169, 23)
After duplication removal #2: (120169, 23)
In [10]:
# choose batches
# batches = [f'batch{i}' for i in range(2,6)]
batches = ['batch1', 'batch2']
batches
Out[10]:
['batch1', 'batch2']

Raw Files Validation¶

  1. How many site tiff files do we have in each folder?
  2. Are all existing files valid? (tif, at least 2049kB, not corrupetd)
In [11]:
root_directory_raw = os.path.join(MOMAPS_DATA_HOME, 'input', 'images', 'raw', 'Opera18DaysReimaged_sorted')

batches_raw = [batch.replace("_16bit_no_downsample","") for batch in batches]
raws = run_validate_folder_structure(root_directory_raw, False, opera18daysREIMAGED_panels, opera18days_markers.copy(),PLOT_PATH, opera18daysREIMAGED_marker_info,
                                    opera18days_cell_lines_to_cond, reps, opera18days_cell_lines_for_disp, opera18days_expected_dapi_raw,
                                     batches=batches_raw, fig_width=15)

batch1

IOPub data rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_data_rate_limit`.

Current values:
ServerApp.iopub_data_rate_limit=1000000.0 (bytes/sec)
ServerApp.rate_limit_window=3.0 (secs)


Total Sites:  82000

========
batch2

IOPub data rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_data_rate_limit`.

Current values:
ServerApp.iopub_data_rate_limit=1000000.0 (bytes/sec)
ServerApp.rate_limit_window=3.0 (secs)


========
====================

Processed Files Validation¶

  1. How many site npy files do we have in each folder? -> How many sites survived the pre-processing?
  2. Are all existing files valid? (at least 100kB, npy not corrupted)
In [12]:
root_directory_proc = os.path.join(MOMAPS_DATA_HOME, 'input', 'images', 'processed', 'Opera18DaysReimaged')
procs = run_validate_folder_structure(root_directory_proc, True, opera18daysREIMAGED_panels, opera18days_markers,PLOT_PATH,opera18daysREIMAGED_marker_info,
                                    opera18days_cell_lines_to_cond, reps, opera18days_cell_lines_for_disp, opera18days_expected_dapi_raw,
                                     batches=batches, fig_width=15)

batch1

IOPub data rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_data_rate_limit`.

Current values:
ServerApp.iopub_data_rate_limit=1000000.0 (bytes/sec)
ServerApp.rate_limit_window=3.0 (secs)


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Total Sites:  53458

========
batch2

IOPub data rate exceeded.
The Jupyter server will temporarily stop sending output
to the client in order to avoid crashing it.
To change this limit, set the config variable
`--ServerApp.iopub_data_rate_limit`.

Current values:
ServerApp.iopub_data_rate_limit=1000000.0 (bytes/sec)
ServerApp.rate_limit_window=3.0 (secs)


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/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep2_r05c11f89p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep2_r05c11f29p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep2_r05c11f42p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep2_r05c11f82p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f66p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f60p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f82p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f65p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f73p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f100p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f37p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f26p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep2_r05c11f58p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f33p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f13p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep2_r05c11f38p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f06p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep2_r05c11f66p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f55p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f19p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f25p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep2_r05c11f76p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f11p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep2_r05c11f90p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f02p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f03p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
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/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep2_r05c11f44p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f32p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
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/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/AGO2, rep1_r04c11f97p01-ch4sk1fk1fl1_panelB_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f92p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f58p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f10p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f49p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f15p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f78p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f18p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f70p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f67p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f97p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f63p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f98p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f19p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f41p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f06p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f37p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f93p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f24p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f44p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f32p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f86p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f76p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f30p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f52p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f33p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f62p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f38p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f66p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f46p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f21p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f12p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f75p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f25p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f81p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f21p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f32p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f99p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f59p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f15p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f28p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f33p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f100p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f49p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f01p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f71p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f28p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f07p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f57p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f23p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f63p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f87p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f19p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f92p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep1_r02c11f46p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f40p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
/home/labs/hornsteinlab/Collaboration/MOmaps/input/images/processed/Opera18DaysReimaged/batch2/SNCA/Untreated/HNRNPA1, rep2_r03c11f20p01-ch4sk1fk1fl1_panelJ_SNCA_processed.npy
Total Sites:  51021

========
====================

Difference between Raw and Processed¶

In [13]:
display_diff(batches, raws, procs, PLOT_PATH, fig_width=15)

batch1

========
batch2

========

Variance in each batch¶

In [14]:
#for batch in list(range(3,9)) + ['7_16bit','8_16bit','9_16bit']:  

for batch in batches:
    with contextlib.redirect_stdout(io.StringIO()):
        var = sample_and_calc_variance(root_directory_proc, batch, 
                                       sample_size_per_markers=200, cond_count=2, rep_count=len(reps), 
                                       num_markers=len(dnls_markers))
    print(f'{batch} var: ',var)

batch1 var:  0.023519648146724494
batch2 var:  0.023363238729173504

filtering qc¶

By order of filtering

1. % site survival after Brenner on DAPI channel¶

Percentage out of the total sites

In [15]:
dapi_filter_by_brenner = show_site_survival_dapi_brenner(df_dapi,batches, opera18days_line_colors, opera18daysREIMAGED_panels,
                                                        figsize=(10,5))

2. % Site survival after Cellpose¶

Percentage out of the sites that passed the previous filter. In parenthesis are absolute values.

A site will be filtered out if Cellpose found 0 cells in it.

In [16]:
dapi_filter_by_cellpose = show_site_survival_dapi_cellpose(df_dapi, batches, dapi_filter_by_brenner, 
                                                           opera18days_line_colors, opera18days_panels, figsize=(15,5))

3. % Site survival by tiling¶

Percentage out of the sites that passed the previous filter. In parenthesis are absolute values.

A site will be filtered out if after tiling, no tile is containing at least 85% of a cell that Cellpose detected.

In [17]:
dapi_filter_by_tiling=show_site_survival_dapi_tiling(df_dapi, batches, dapi_filter_by_cellpose, 
                                                     opera18days_line_colors, opera18daysREIMAGED_panels, figsize=(15,5))

4. % Site survival after Brenner on target channel¶

Percentage out of the sites that passed the previous filter. In parenthesis are absolute values (if different than the percentages).

In [18]:
show_site_survival_target_brenner(df_dapi, df_target, dapi_filter_by_tiling,
                                 figsize=(15,8), markers=opera18days_markers)

Numbers!¶

  1. Total number of tiles: for each condition, we can know how many tiles we have --> number of data points for the model to train and infer on --> number of points in UMAPs..
  2. Total number of whole cells: for each condtion, we can know how many whole cells we have
In [19]:
names = ['Total number of tiles', 'Total number of whole cells']
stats = ['n_valid_tiles','site_whole_cells_counts_sum','site_cell_count','site_cell_count_sum']
total_sum = calc_total_sums(df_target, df_dapi, stats)
    

# for stat, name in zip(stats[:2], names):
#     to_heatmap = total_sum.rename(columns={stat:'index'})
#     plot_filtering_heatmap(to_heatmap, extra_index='marker', vmin=None, vmax=None,
#                           xlabel = name, show_sum=True, figsize=(4,8))
In [20]:
total_sum.sum()
Out[20]:
batch                          batch1batch1batch1batch1batch1batch1batch1batc...
cell_line_cond                 FUSHeterozygous UntreatedFUSHeterozygous Untre...
rep                            rep1rep2rep1rep2rep1rep2rep1rep2rep1rep2rep1re...
panel                          panelApanelApanelApanelApanelApanelApanelApane...
n_valid_tiles                                                             144424
site_whole_cells_counts_sum                                             159443.0
site_cell_count                                                         500265.0
site_cell_count_sum                                                     894423.0
marker                         G3BP1G3BP1G3BP1G3BP1G3BP1G3BP1G3BP1G3BP1G3BP1G...
dtype: object
In [21]:
show_total_sum_tables(total_sum)
n_valid_tiles % valid tiles site_whole_cells_counts_sum site_cell_count
batch1
count 460.000000 460.000000 460.000000 460.000000
mean 167.563043 1.675630 192.236957 580.289130
std 114.145601 1.141456 215.350893 508.077612
min 15.000000 0.150000 15.000000 35.000000
25% 99.750000 0.997500 100.750000 298.000000
50% 155.500000 1.555000 159.000000 523.000000
75% 214.250000 2.142500 225.000000 777.000000
max 1059.000000 10.590000 2375.000000 5325.000000
sum 77079.000000 NaN 88429.000000 266933.000000
expected_count 450.000000 450.000000 450.000000 450.000000
n_valid_tiles % valid tiles site_whole_cells_counts_sum site_cell_count
batch2
count 460.000000 460.000000 460.000000 460.000000
mean 146.402174 1.464022 154.378261 507.243478
std 81.780441 0.817804 103.014395 333.653626
min 8.000000 0.080000 9.000000 8.000000
25% 85.000000 0.850000 87.000000 258.750000
50% 135.000000 1.350000 136.000000 460.000000
75% 200.250000 2.002500 207.000000 732.000000
max 658.000000 6.580000 952.000000 2796.000000
sum 67345.000000 NaN 71014.000000 233332.000000
expected_count 450.000000 450.000000 450.000000 450.000000
n valid tiles % valid tiles site_whole_cells_counts_sum site_cell_count
All batches
count 920.000000 920.000000 920.000000 920.000000
mean 156.982609 1.569826 173.307609 543.766304
std 99.799645 0.997996 169.769523 431.124290
min 8.000000 0.080000 9.000000 8.000000
25% 90.750000 0.907500 93.000000 281.000000
50% 142.000000 1.420000 145.500000 505.000000
75% 206.000000 2.060000 213.000000 760.000000
max 1059.000000 10.590000 2375.000000 5325.000000
sum 144424.000000 NaN 159443.000000 500265.000000
expected_count 450.000000 450.000000 450.000000 450.000000

Number of Cells in Site for each batch and cell line¶

In [22]:
df_no_empty_sites = df_dapi[df_dapi.n_valid_tiles !=0]
plot_cell_count(df_no_empty_sites, opera18days_lines_order, opera18days_custom_palette, y='site_cell_count_sum', 
                title='Cell Count Average per Site (from tiles)')

plot_cell_count(df_no_empty_sites, opera18days_lines_order, opera18days_custom_palette, y='site_whole_cells_counts_sum',
                title='Whole Cell Count Average per Site')

plot_cell_count(df_no_empty_sites, opera18days_lines_order, opera18days_custom_palette, y='site_cell_count',
               title='Cellpose Cell Count Average per Site')

number of valid tiles per image (site)¶

In [23]:
plot_catplot(df_dapi, opera18days_custom_palette,reps, x='n_valid_tiles', x_title='valid tiles count', batch_min=1, batch_max=1)

Heatmap QC per batch, panel and cell line(tiles that passed QC condition) ¶

In [24]:
plot_hm(df_dapi, split_by='rep', rows='cell_line_cond', columns='panel')

Assessing Staining Reproducibility and Outliers¶

In [25]:
# for batch in batches:
#     print(batch)
#     #batch_num = batch.replace('batch',"")
#     run_calc_hist_new(f'FUS_lines_stress_2024_sorted/{batch}', opera18days_cell_lines_for_disp, opera18days_markers, 
#                            hist_sample=10,sample_size_per_markers=200, ncols=8, nrows=4, dnls=True)
#     print("="*30)
In [ ]:
# save notebook as HTML ( the HTML will be saved in the same folder the original script is)
from IPython.display import display, Javascript
display(Javascript('IPython.notebook.save_checkpoint();'))
os.system('jupyter nbconvert --to html src/preprocessing/notebooks/no_ds/qc_report_newPP_Opera18dREIMAGED.ipynb')
In [ ]: